On 8/17/12 6:44 PM, Acoot Brett wrote:
This explaination of Justin is correct. For VMD read trr file, it cannot read
more than 522 frames, and it can read far more than 522 frames of xtc file.
However if the XTC is too large, VMD will gives the error of runtime error. Can
anyone solve this p
,
Acoot
- Original Message -
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Saturday, 18 August 2012 8:17 AM
Subject: Re: [gmx-users] xtc file and trr file
On 8/17/12 5:52 PM, Acoot Brett wrote:
> Dear Justin,
>
> But it is very dif
On 8/17/12 5:52 PM, Acoot Brett wrote:
Dear Justin,
But it is very difficult to explain why the xtc file gives more frames in VMD
than trr file. Can you explain it? Or VMD has made the modification when read
the xtc file or the trr file?
It is possible that VMD ran out of memory attemptin
; Discussion list for GROMACS users
Cc:
Sent: Saturday, 18 August 2012 7:39 AM
Subject: Re: [gmx-users] xtc file and trr file
On 8/17/12 4:33 PM, Acoot Brett wrote:
> Dear All,
>
> Follwong is the MD mdp file I used for my production MD, which I downloaded
> from
> http://www.bevanlab
ection
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off
- Forwarded Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Friday, 17 August 2012 8:41 PM
Subject: Re: [gmx-users] xtc fi
: Discussion list for GROMACS users
Cc:
Sent: Friday, 17 August 2012 8:41 PM
Subject: Re: [gmx-users] xtc file and trr file
On 17/08/2012 6:46 PM, Acoot Brett wrote:
> Dear All,
>
> After a production MD, both the xtc file and trr file are produced. trr file
> is much larger than the xtc fi
On 17/08/2012 6:46 PM, Acoot Brett wrote:
Dear All,
After a production MD, both the xtc file and trr file are produced. trr file is
much larger than the xtc file. But when we openned the original gro file one of
the file from xtc file and trr file in VMD, we will find the xtc contains more
fr
On Fri, Aug 17, 2012 at 2:16 PM, Acoot Brett wrote:
>
> Dear All,
>
> After a production MD, both the xtc file and trr file are produced. trr
> file is much larger than the xtc file. But when we openned the original gro
> file one of the file from xtc file and trr file in VMD, we will find the xtc
Dear All,
After a production MD, both the xtc file and trr file are produced. trr file is
much larger than the xtc file. But when we openned the original gro file one of
the file from xtc file and trr file in VMD, we will find the xtc contains more
frames in comparison with the trr file.
Will
Hi João, I don't remember EM runs ever producing .xtc files, maybe to
prevent people to use them when "grompp'ing" in the next step. (they're at
much lower precision)
Anyway, that would be nice in case you want to see what's going on during
EM.
On Fri, Jan 7, 2011 at 7:02 PM, João Rodrigues wro
Hello all,
I'm trying to run energy minimization on my system (protein complex). Since
it's a bit big (produces 2GB of trr files using l-bfgs) I'm trying to
supress most of this output and replace the trr file with an xtc file.
I'm using these options in my mdp file (output related):
nstxout
- Original Message -
From: "Justin A. Lemkul"
Date: Sunday, May 23, 2010 13:49
Subject: Re: [gmx-users] xtc file
To: Discussion list for GROMACS users
>
>
> Moeed wrote:
> >Dear experts,
> >
> >I am trying to exclude all nonbonded interaction on
Moeed wrote:
Dear experts,
I am trying to exclude all nonbonded interaction on hexane molecule.
1-For the md -rerun command I do not know how to get the input XTC file.
the program is expecting rerun.xtc
mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o
ORIGINAL-Trajectory-NO
Dear experts,
I am trying to exclude all nonbonded interaction on hexane molecule.
1-For the md -rerun command I do not know how to get the input XTC file. the
program is expecting rerun.xtc
mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o
ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-
Thank you very much for your replay sir...
On Wed, Apr 14, 2010 at 5:36 AM, Justin A. Lemkul wrote:
>
>
> Bharath.K. Chakravarthi wrote:
>
>> sir should i set dat to 0 or what to do
>>
>>
> I clearly stated that you should set nstxtcout > 0 in my first message.
> Leaving any output control
Bharath.K. Chakravarthi wrote:
sir should i set dat to 0 or what to do
I clearly stated that you should set nstxtcout > 0 in my first message. Leaving
any output control parameter set to zero means "produce output every zero steps"
or essentially, not at all.
-Justin
On Wed, Apr
sir should i set dat to 0 or what to do
On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi <
bharath.chakravar...@gmail.com> wrote:
>
>
> On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi <
> bharath.chakravar...@gmail.com> wrote:
>
>> Thank you for your kind replay sir
>> s
Bharath.K. Chakravarthi wrote:
Thank you for your kind replay sir
sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is
set to 500
is this what u told...
No, this is not what I said. These are different settings entirely. nstxout is
for the .trr file, nstxtcout is
Thank you for your kind replay sir
sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set
to 500
is this what u told...
i have also attached the .mdp file in this mail sir
On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul wrote:
>
>
> Bharath.K. Chakravarthi wrote:
>
>>
On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi <
bharath.chakravar...@gmail.com> wrote:
> Thank you for your kind replay sir
> sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is
> set to 500
> is this what u told...
> i have also attached the .mdp file in this m
Bharath.K. Chakravarthi wrote:
hi there
i tried to run MD and i wanted to use *.xtc file in vmd to visualize the
protein but unfortunately there is no such file
i given the command like this
mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c
md_final.gro -e md_ener.edr
as proce
hi there
i tried to run MD and i wanted to use *.xtc file in vmd to visualize the
protein but unfortunately there is no such file
i given the command like this
mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro
-e md_ener.edr
as procedure this should create md_traj.xtc fil
Thank you .
Carla
On Tue, Jan 26, 2010 at 11:53 AM, Carsten Kutzner wrote:
>
> On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote:
>
> > Hi everyone,
> >
> > Please I'm having a problem with mdrun:
> > If I type:
> > mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g
> test.lo
On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote:
> Hi everyone,
>
> Please I'm having a problem with mdrun:
> If I type:
> mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g
> test.log
>
> I never get the .xtc file. Can anyone tell me why & what can I do to have an
> .x
Hi everyone,
Please I'm having a problem with mdrun:
If I type:
mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g
test.log
I never get the .xtc file. Can anyone tell me why & what can I do to have an
.xtc file?
Thank you
Carla
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